Legal consequences of resignation in a limited labour contract

Good day,

My situation is that I submitted my resignation last October 5 effectivity same day, in hard copy.

I also emailed it to my manager and sent it on WhatsApp to my boss and manager. They saw my resignation in WhatsApp but my manager doesn't accept my hard copy because he said that he doesn’t want to have problems.

So, I messaged my boss through WhatsApp and he doesn't seem to care about it. They told me that I have to pay the visa cost before they give me my passport.

I talked to the Labor Department and they said I should only pay my employer 45 days of my salary, and I am willing to pay the 45-day salary for resignation but my boss is asking to for the visa cost also. He said he knows his rights and I must pay more than just the 45 days salary.

Please help me, I don't know what to do. I need to get back urgently to the Philippines.